In 2008, the Etheostoma percnurum species complex was described as 4 distinct species by Rebecca E. Blanton and Robert E. Jenkins.1 The 4 species within the complex are:

Etheostoma percnurum (Jenkins 1994) found in the Clinch River system of the Tennessee River drainage.

Etheostoma marmorpinnum (Blanton & Jenkins 2008) found in the Little River system of the Tennessee River drainage.

Etheostoma sitikuense (Blanton 2008) found in the Little Tennessee River system of the Tennessee River drainage.

Etheostoma lemniscatum (Blanton 2008) found in the Big South Fork system of the Cumberland River drainage.

These 4 species were described as genetically and meristically distinct and were elevated to specis status. However, all species within the complex are federally listed as endangered under the species name Etheostoma percnurum by USFWS and the ESA of 1973.

This work is funded by USFWS to look at the genetic diversity of 3 of the species within the complex: E. percnurum, E. marmorpinnum, and E. lemniscatum.

1 Blanton, R. E., and R. E. Jenkins. 2008. Three new darter species of the Etheostoma percnurum complex (Percidae, subgenus Catonotus) from the Tennessee and Cumberland river drainages. Zootaxa 1963: 1-24.


Genetic diversity of a highly imperiled, habitat specialist, Etheostoma marmorpinnum, from Little River, TN

Jacob F. Brumley and Rebecca E. Blanton
Austin Peay State University, Department of Biology and Center of Excellence for Field Biology
Figure 1. Etheostoma marmorpinnum from Little River at River John’s

Figure 1. Etheostoma marmorpinnum from Little River at River John’s

Introduction

Habitat loss and fragmentation cause declines in population connectivity and abundance, which contributes to genetic drift and loss of genetic diversity.1,2,3 Decreases in abundance and genetic diversity can lead to inbreeding and genetic homogenization of the population, reducing fitness of both the individuals and the population as a whole.2,3,4,5 The federally endangered Marbled Darter, Etheostoma marmorpinnum, (Fig. 1) is found in the Little River in Tennessee. Although once known in the South Fork Holston River, the darter is now found in only a 20 rkm stretch of the lower Little River and is restricted in range both upstream and downstream by dams. Its restricted range, patchy habitat, small population size, and limited larval dispersal make this species highly susceptible to further habitat loss or degradation. Genetic monitoring protocols can establish a genetic diversity baseline and track changes in genetic diversity over time. Such temporal measures of genetic diversity can be specifically linked to changes in habitat or to management practices to determine how such changes have impacted genetic diversity.6,7 Genetic diversity of E. marmorpinnun has not been previously estimated, despite past population loss, propagation, and reintroductions.

Objectives

  1. Estimate genetic diversity at site and species levels.

  2. Provide a genetic baseline for conservation and future genetic monitoring.

Methods and Materials

  1. Fin clips collected during snorkel surveys at 3 locatlities in lower Little River, spanning current range of species (Fig. 2, 3, 4)

  2. Six variable microsatellite loci optimized for PCR amplification from a set of 20 primers produced for Etheostoma lemniscatum

  3. R(3.5.1) used to run a standard suite of population genetic analyses to estimate genetic diversity and population structure (Table 1)

Figure 2. Blount County, TN.

Figure 3. Collection sites on Little River, TN. Sites 1 & 3 represent the downstream and upstream extents of the known range.

Figure 3. Collection sites on Little River, TN. Sites 1 & 3 represent the downstream and upstream extents of the known range.

Figure 4. Satellite image of site locations.

Table 1. Packages used for genetic analyses
Packages Dependencies Analyses
PopGenReport adegenet/ade4 AR, Na, Ho, He, Fst, Private Alleles, Null Alleles, Deviations from HWE
diveRsity AR, Na, Ho, He, Fst, Fis, Private Alleles, Null Alleles, Deviations from HWE
hierfstat adegenet/ade4 Fst, Fis, pairwise Fst
genepop LD

Results

Captured and clipped 56 individuals of 117 observed during snorkel surveys.

Figure 5. Interactive map of sites and individuals clipped per site.

Linkage Disequilibrium: There is no evidence of consistent LD between locus pairs.

Deviation from Hardy-Weinberg Equilibrium: There is no evidence of deviations from HWE.

Locus Variability: Allele counts ranged from 2 to 9 alleles per locus.

Private Alleles: 4 private alleles were counted (2 at TN-33 Bridge; 2 at Coulter’s Bridge).

Population-Genetic Metrics:

Allelic Richness (AR): Mean AR ranged between sites from 3.204 to 3.430.

Mean Allele per Locus (Na):

Figure 6. Mean alleles per locus (Na) for each site.

Observed Heterozygosity (Ho):

Figure 7. Observed Heterozygosity (Ho) for each site.

Inbreeding Coefficients (FIS): FIS for the species is 0.0503.

Figure 8. Inbreeding coefficients (FIS) for each site with 95% CI; asterisk denotes significance at Coulter’s Bridge.

Fixation Indices:

Fixation (FST): FST for the species is 0.0297.

Pairwise FST:

Table 2. Pairwise Fst between sites.
TN-33 Bridge River John’s Coulter’s Bridge
TN33 – – –
RJ 0.119 – –
CB 0.043 0.028 –

Discussion

Etheostoma marmorpinnum has low genetic diversity and may have reduced adaptive potential.8 However, E. marmorpinnum populations are not isolated, suggesting yearly transfer of genetic material throughout it’s range. There is evidence of inbreeding within the Coulter’s Bridge population that may reflect past propagation and reintroducation to this area or the site’s upstream location. Populations at the upstream extent of a species’ range often show decreases in genetic diversity due to increased isolation, associated with reduced upstream dispersal.9,10,11 To protect the species from further loss of genetic diversity and to combat inbreeding potential, we recommend future genetic monitoring that specifically examines the effects of habitat changes or future conservation actions such as reintroductions or translocations. Such monitoring can help ensure population connectivity is maintained and actions do not have unintended effects of lowering genetic diversity overall. Continuing efforts include collection of genotypic data for the remaining 14 loci to provide more robust estimates of genetic diversity and population structure and to estimate effective population size.

Literature Cited

1 Farhig, L. 1997. Relative effects of habitat loss and fragmentation on population extinction. The Journal of Wildlife Management 61: 603-610.

2 Johannesson, K. and C. Andre. 2006. Life on the margin: genetic isolation and diversity loss in a peripheral marine ecosystem, the Baltic Sea. Molecular Ecology 15: 2013-2029.

3 Thrush, S. F., J. Halliday, J. E. Hewitt, and A. H. Lohrer. 2008. The effects of habitat loss, fragmentation, and community homogenization on resilience in estuaries. Ecological Applications 18: 12-21.

4 Frankham, R. 1996. Relationships of genetic variation to population size in wildlife. Conservation Biology 10: 1500-1508.

5 Reed, D. H. and R. Frankham. 2003. Correlation between fitness and genetic diversity. Conservation Biology 17: 230-237.

6 Schwartz, M. K., G. Luikart, and R. S. Waples. 2006. Genetic monitoring as a promising tool for conservation management. TRENDS in Ecology and Evolution 22: 25-33.

7 Hansen, M. M., I. Olivieri, D. M. Waller, E. E. Nielsen, and the GeM Working Group. 2012. Monitoring adaptive genetic responses to environmental change. Molecular Ecology 21: 1311-1329.

8 Frankham, R. 1995. Conservation genetics. Annual Review of Genetics 29: 305-327.

9 Morrissey, M. B., and D. T. de Kerckhove. 2009. The maintenance of genetic variation due to asymmetric gene flow in dendritic metapopulations. The American Naturalist 174: 875-889.

10 Paz-Vinas, I., G. Loot, V. M. Stevens, and S. Blanchet. 2015. Evolutionary processes driving spatial patterns of intraspecific genetic diversity in river ecosystems. Molecular Ecology 24: 4586-4604.

11 Thomaz, A. T., M. R. Christie, and L. L. Knowles. 2016. The architecture of river networks can drive the evolutionary dynamics of aquatic populations. Evolution 70: 731-739.

Acknowledgements

We thank Conservation Fisheries, Inc. (P. Rakes and C. Ruble) and N. Disotell for their extraordinary assistance in the field; USFWS for funding this project; APSU Center of Excellence for Field Biology for equipment; The home owners and River John’s for access to the Little River.


Impacts of habitat loss on the genetic diversity and effective population size of Etheostoma lemniscatum, the Tuxedo Darter

Jacob F. Brumley, Rebecca E. Blanton, and Mollie F. Cashner
Austin Peay State University, Department of Biology and Center of Excellence for Field Biology

Figure 2. McCreary County, KY and Scott County, TN.

Figure 3. Satellite image of site locations.


Hanging on for life: genetic diversity of the endangered Duskytail Darter, Etheostoma percnurum

Jacob F. Brumley and Rebecca E. Blanton
Austin Peay State University, Department of Biology and Center of Excellence for Field Biology

Figure 2. Scott County, VA.

Figure 3. Satellite image of site locations.